Proteomics Portrait of Archival Lesions of Chronic Pancreatitis

Chronic pancreatitis is a chronic inflammatory disorder of the pancreas. The etiology is multi-fold, but all lead to progressive scarring and loss of pancreatic function. Early diagnosis is difficult; and the understanding of the molecular events that underlie this progressive disease is limited. In this study, we investigated differential proteins associated with mild and severe chronic pancreatitis in comparison with normal pancreas and pancreatic cancer. Paraffin-embedded formalin-fixed tissues from five well-characterized specimens each of normal pancreas (NL), mild chronic pancreatitis (MCP), severe chronic pancreatitis (SCP) and pancreatic ductal adenocarcinoma (PDAC) were subjected to proteomic analysis using a “label-free” comparative approach. Our results show that the numbers of differential proteins increase substantially with the disease severity, from mild to severe chronic pancreatitis, while the number of dysregulated proteins is highest in pancreatic adenocarcinoma. Important functional groups and biological processes associated with chronic pancreatitis and cancer include acinar cell secretory proteins, pancreatic fibrosis/stellate cell activation, glycoproteins, and inflammatory proteins. Three differential proteins were selected for verification by immunohistochemistry, including collagen 14A1, lumican and versican. Further canonical pathway analysis revealed that acute phase response signal, prothrombin activation pathway, and pancreatic fibrosis/pancreatic stellate cell activation pathway were the most significant pathways involved in chronic pancreatitis, while pathways relating to metabolism were the most significant pathways in pancreatic adenocarcinoma. Our study reveals a group of differentially expressed proteins and the related pathways that may shed light on the pathogenesis of chronic pancreatitis and the common molecular events associated with chronic pancreatitis and pancreatic adenocarcinoma

Pancreatic Cancer Susceptibility Loci and Their Role in Survival

Pancreatic cancer has one of the worst mortality rates of all cancers. Little is known about its etiology, particularly regarding inherited risk. The PanScan project, a genome-wide association study, identified several common polymorphisms affecting pancreatic cancer susceptibility. Single nucleotide polymorphisms (SNPs) in ABO, sonic hedgehog (SHH), telomerase reverse transcriptase (TERT), nuclear receptor subfamily 5, group A, member 2 (NR5A2) were found to be associated with pancreatic cancer risk. Moreover the scan identified loci on chromosomes 13q22.1 and 15q14, to which no known genes or other functional elements are mapped. We sought to replicate these observations in two additional, independent populations (from Germany and the UK), and also evaluate the possible impact of these SNPs on patient survival. We genotyped 15 SNPs in 690 cases of pancreatic ductal adenocarcinoma (PDAC) and in 1277 healthy controls. We replicated several associations between SNPs and PDAC risk. Furthermore we found that SNP rs8028529 was weakly associated with a better overall survival (OS) in both populations. We have also found that NR5A2 rs12029406_T allele was associated with a shorter survival in the German population. In conclusion, we found that rs8028529 could be, if these results are replicated, a promising marker for both risk and prognosis for this lethal disease

Assessment and optimisation of normalisation methods for dual-colour antibody microarrays

<p>Abstract</p> <p>Background</p> <p>Recent advances in antibody microarray technology have made it possible to measure the expression of hundreds of proteins simultaneously in a competitive dual-colour approach similar to dual-colour gene expression microarrays. Thus, the established normalisation methods for gene expression microarrays, e.g. loess regression, can in principle be applied to protein microarrays. However, the typical assumptions of such normalisation methods might be violated due to a bias in the selection of the proteins to be measured. Due to high costs and limited availability of high quality antibodies, the current arrays usually focus on a high proportion of regulated targets. Housekeeping features could be used to circumvent this problem, but they are typically underrepresented on protein arrays. Therefore, it might be beneficial to select invariant features among the features already represented on available arrays for normalisation by a dedicated selection algorithm.</p> <p>Results</p> <p>We compare the performance of several normalisation methods that have been established for dual-colour gene expression microarrays. The focus is on an invariant selection algorithm, for which effective improvements are proposed. In a simulation study the performances of the different normalisation methods are compared with respect to their impact on the ability to correctly detect differentially expressed features. Furthermore, we apply the different normalisation methods to a pancreatic cancer data set to assess the impact on the classification power.</p> <p>Conclusions</p> <p>The simulation study and the data application demonstrate the superior performance of the improved invariant selection algorithms in comparison to other normalisation methods, especially in situations where the assumptions of the usual global loess normalisation are violated.</p

Sequence-selective detection of double-stranded DNA sequences using pyrrole-imidazole polyamide microarrays

We describe a microarray format that can detect double-stranded DNA sequences with a high degree of sequence selectivity. Cyclooctyne-derivatized pyrrole-imidazole polyamides were immobilized on azide-modified glass substrates using microcontact printing and a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. These polyamide-immobilized substrates selectively detected a seven-base-pair binding site incorporated within a double-stranded oligodeoxyribonucleotide sequence even in the presence of an excess of a sequence with a single-base-pair mismatc

Shot at Dawn: Late Photography and the Anti-War Memorial

The military executions of World War One are the subject of Chloe Dewe Mathews’s 2014 photographic series Shot at Dawn. These events—in which hundreds of soldiers were court-martialled and executed for cowardice and desertion—remain controversial, without consensus or established collective narrative. This article charts historic negotiations with the subject but also considers more recent efforts to integrate these proceedings within memorial practice. World War One remembrance activities, whilst diverse, have often emphasised sacrifice, heroism and community. Correspondingly, participation and engagement were core values in the major British World War One centenary arts project, titled 14-18 NOW, from which Shot at Dawn was commissioned. Chloe Dewe Mathews’s contribution to the programme, however, presents a photographic aesthetic of resistance to the principles of inclusivity and remembrance elsewhere embraced by the project. As such, the work challenges the consensual politics of commemoration and—through the practices of late photography, land art and performance pilgrimage— substitutes trauma and forgetfulness for reconciliation and memory

Exciton states and optical properties of CdSe nanocrystals

The optical spectra of CdSe nanocrystals up to 55 A in diameter are analyzed in a wide range of energies from the fine structure of the low-energy excitations to the so-called high-energy transitions. We apply a symmetry-based method in two steps. First we take the tight-binding (TB) parameters from the bulk sp^{3}s^{*} TB model, extended to include the spin-orbit interaction. The full single-particle spectra are obtained from an exact diagonalization by using a group-theoretical treatment. The electron-hole interaction is next introduced: Both the Coulomb (direct) and exchange terms are considered. The high-energy excitonic transitions are studied by computing the electric dipole transition probabilities between single-particle states, while the transition energies are obtained by taking into account the Coulomb interaction. The fine structure of the lowest excitonic states is analyzed by including the electron-hole exchange interaction and the wurtzite crystal-field terms in the exciton Hamiltonian. The latter is diagonalized in the single electron-hole pair excitation subspace of progressively increasing size until convergence. The peaks in the theoretical transition spectra are then used to deduce the resonant and nonresonant Stokes shifts, which are compared with their measured values in photoluminescence experiments. We find that the final results depend on the crystal-field term, the relative size of the surface and the degree of saturation of the dangling bonds. The results show a satisfactory agreement with the available experimental data.Comment: Revtex, 24 pages, 7 Postscript figure

Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing

The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is significant because it shows that next generation sequencing and motif finding informatics have the potential to simplify the selection of aptamers by avoiding multiple rounds of enzymatic transcription and amplification